Structure of PDB 5vp2 Chain 20

Receptor sequence

>5vp220 (length=83) Species: 300852 (Thermus thermophilus HB8)

AHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNV
GMGRDFTLFALVDGVVEFQDRGRLGRYVHVRPL

3D structure

• PDB: 5vp2 Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
• Chain: 20
• Resolution: 2.8 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	20	A2 H3 K4 S9 T10 R11 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 G54 R55 D56 F57 F69 R74 L75 R77	A1 H2 K3 S8 T9 R10 N11 R13 D14 S15 Q16 A17 K18 R19 K23 R24 Y25 E26 Q28 R31 A32 G33 N34 I35 R38 R40 G41 T42 G53 R54 D55 F56 F68 R73 L74 R76
BS02	rna	20	R72 G73 R74 L75	R71 G72 R73 L74

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5vp2, PDBe:5vp2, PDBj:5vp2
• PDBsum: 5vp2
• PubMed: 28505372
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)